During the last 30 years the deep Eastern Mediterranean Sea has been the focus of a number of oceanographic studies funded either from the EU and/or from various national research initiatives. In this review we attempt to summarise some of the major outcomes of this research regarding the environmental factors that influence its deep benthic communities. Benthic components such as microbiota, meiofauna, macrofauna and megafauna are investigated under the prism of knowledge acquired gradually, based on the evolution of both modern sampling techniques as well as laboratory analytical capabilities. In all cases, it was found that food availability is a key factor shaping the structure of these communities. Secondarily, it was sediment texture that also played a key role, mainly with regards to the larger benthic components. Processes such as dense shelf water cascading, fluctuations in surface productivity due to various environmental forcings are presented in order to understand how potential benthic responses are elicited. Last but not least we feature the recent findings regarding the ecological services provided by hydrocarbon-degrading bacterial consortia in the biodegradation of crude oil constituents. Since the area is already under enormous anthropogenic pressures and is very soon bound to experience intense oil and gas extraction activities, this review comes as a reminder to stress its vulnerability. •30 years of deep-sea research in the Eastern Mediterranean are reviewed.•Benthic components such as microbiota, meiofauna, macrofauna and megafauna primarily depend on food availability.•Environmental forcings influence key processes triggering the response of benthic communities.•Hydrocarbon-degrading bacteria may provide significant ecological services in the biodegradation of crude oil contamination.